1E0J | pdb_00001e0j

gp4d helicase from phage T7 ADPNP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.304 (Depositor) 
  • R-Value Work: 
    0.253 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1E0J

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of T7 Gene 4 Ring Helicase Indicates a Mechanism for Sequential Hydrolysis of Nucleotides

Singleton, M.R.Sawaya, M.R.Ellenberger, T.Wigley, D.B.

(2000) Cell 101: 589

  • DOI: https://doi.org/10.1016/s0092-8674(00)80871-5
  • Primary Citation Related Structures: 
    1E0J, 1E0K

  • PubMed Abstract: 

    We have determined the crystal structure of an active, hexameric fragment of the gene 4 helicase from bacteriophage T7. The structure reveals how subunit contacts stabilize the hexamer. Deviation from expected six-fold symmetry of the hexamer indicates that the structure is of an intermediate on the catalytic pathway. The structural consequences of the asymmetry suggest a "binding change" mechanism to explain how cooperative binding and hydrolysis of nucleotides are coupled to conformational changes in the ring that most likely accompany duplex unwinding. The structure of a complex with a nonhydrolyzable ATP analog provides additional evidence for this hypothesis, with only four of the six possible nucleotide binding sites being occupied in this conformation of the hexamer. This model suggests a mechanism for DNA translocation.


  • Organizational Affiliation
    • Sir William Dunn School of Pathology, University of Oxford, United Kingdom.

Macromolecule Content 

  • Total Structure Weight: 192.65 kDa 
  • Atom Count: 13,392 
  • Modeled Residue Count: 1,726 
  • Deposited Residue Count: 1,734 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
DNA HELICASE
A, B, C, D, E
A, B, C, D, E, F
289Escherichia phage T7Mutation(s): 0 
Gene Names: GENE 4
EC: 5.6.2.3 (UniProt), 2.7.7 (UniProt)
UniProt
Find proteins for P03692 (Escherichia phage T7)
Explore P03692 
Go to UniProtKB:  P03692
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03692
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ANP

Query on ANP



Download:Ideal Coordinates CCD File
G [auth A],
I [auth B],
K [auth D],
M [auth E]
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth D],
N [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.304 (Depositor) 
  • R-Value Work:  0.253 (Depositor), 0.244 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.18α = 90
b = 119.18β = 90
c = 283.42γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-06-09
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other